arXiv subjects

Alireza Moradzadeh

Publications and source records attributed to Alireza Moradzadeh.

5 recordsLinked to original sources

arXiv2026

Native Multi-Dimensional Subquadratic Operators via Input Dependent Long Convolutions

Subquadratic alternatives to attention require compromises when applied to multi-dimensional data: standard convolutions lack global receptive fields and input dependency, while recurrent models require rasterizing data such as images, volumes, and partial differential equation (PDE) into an ad-hoc $1\rm D$ scan order that violates their spatial structure. We introduce \textit{HyenaND}, a subquadratic, global, input-dependent operator that acts directly on the native geometry of multidimensional data through convolutions with implicitly parametrized global, input-dependent multi-dimensional convolutional kernels. Our CUDA implementation, \texttt{nSubQ}, fuses the FFT-convolution path to turn HyenaND's $\mathcal{O}(L \log L)$ scaling into wall-clock speedups. Across long-context genomics, computer vision, medical imaging, and PDE modeling, pure HyenaND stacks match the accuracy of strong attention baselines, while hybrid configurations that interleave HyenaND and attention layers outperform both pure attention and strong recurrence-based hybrids.

cs.LG↗

arXiv2026

Structure of the Circular-Dyadic Convolution Error

Dyadic and circular convolution can both be computed in $O(N\log N)$ time using the Hadamard transform and the FFT-computed discrete Fourier transform (DFT), respectively. The Hadamard transform is preferable for its real-valued sign flips, yet its substitution for the DFT introduces algebraic error. We present three complementary results that characterize this error. First, we identify exact error cancellation: two input and two output positions are universally error-free, and no reordering of the output can eliminate this error. Second, the error operator is nearly full rank, while its null space has only logarithmic dimension. Third, the expected error is governed by a single alignment scalar, with a closed-form expression obtained by averaging over random filters. In general, the substitution error asymptotically doubles the output energy, except for filters in the universal zero-error subspace, which incur no error. Collectively, these results show that the substitution error is structured, predictable, and governed by alignment.

cs.LG↗

arXiv2025

Want to train KANS at scale? Now UKAN!

Kolmogorov-Arnold Networks (KANs) have recently emerged as a powerful alternative to traditional multilayer perceptrons. However, their reliance on predefined, bounded grids restricts their ability to approximate functions on unbounded domains. To address this, we present Unbounded Kolmogorov-Arnold Networks (UKANs), a method that removes the need for bounded grids in traditional Kolmogorov-Arnold Networks (KANs). The key innovation of this method is a coefficient-generator (CG) model that produces, on the fly, only the B-spline coefficients required locally on an unbounded symmetric grid. UKANs couple multilayer perceptrons with KANs by feeding the positional encoding of grid groups into the CG model, enabling function approximation on unbounded domains without requiring data normalization. To reduce the computational cost of both UKANs and KANs, we introduce a GPU-accelerated library that lowers B-spline evaluation complexity by a factor proportional to the grid size, enabling large-scale learning by leveraging efficient memory management, in line with recent software advances such as FlashAttention and FlashFFTConv. Performance benchmarking confirms the superior memory and computational efficiency of our accelerated KAN (warpKAN), and UKANs, showing a 3-30x speed-up and up to 1000x memory reduction compared to vanilla KANs. Experiments on regression, classification, and generative tasks demonstrate the effectiveness of UKANs to match or surpass KAN accuracy. Finally, we use both accelerated KAN and UKAN in a molecular property prediction task, establishing the feasibility of large-scale end-to-end training with our optimized implementation.

cs.LG↗

arXiv2025

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

cs.LG↗

arXiv2022

Topology-based Phase Identification of Bulk, Interface, and Confined Water using Edge-Conditioned Convolutional Graph Neural Network

Water plays a significant role in various physicochemical and biological processes. Understanding and identifying water phases in various systems such as bulk, interface, and confined water is crucial in improving and engineering state-of-the-art nano-devices. Various order parameters have been developed to distinguish water phases, including bond-order parameters, local structure index, and tetrahedral order parameters. These order parameters are often developed with the assumption of homogenous bulk systems, while most applications involve heterogeneous and non-bulk systems, thus, limiting their generalizability. Our study develops a methodology based on the graph neural network to distinguish water phases directly from data and to learn features instead of predefining them. We provide comparisons between baseline methods trained using conventional order-parameters as features, and a graph neural network model trained using radial distance and hydrogen-bonding information for phase classification and phase transition of water in bulk, interface, and confined systems with continuous and discontinuous phase transitions.

physics.comp-ph↗